Multiscale Modeling Tools for Structural Biology
From BTRR
Overview
Problems in structural biology increasingly require researchers to move between models of low resolution and detailed atomic models to fully explore and exploit experimental information. This resource focuses on development of new and integrated approaches to multiscale modeling, with an emphasis on modeling large-scale assemblies of nucleic acids and proteins with nucleic acids, developing methods that combine lattice-based dynamic Monte Carlo and all-atom molecular dynamics, studying physical processes involved in and developing models for the interactions associated with virus assembly, and establishing new tools for the combined treatment of crystallographic and low-resolution structural models from cryo-electron microscopy. These research threads are tied together through the development and distribution of computer codes to make such multiscale simulations and modeling readily accessible to the scientific community at large.
Current Research
Current research involves modeling very large conformational changes occurring in proteins, nucleic acids, and their assemblies; developing methods and models to explore virus swelling and associated large-scale capsid dynamics during viral maturation; exploring meso-scale distortions of molecular assemblies with the use of low-resolution data from electron microscopy, in the absence of any atomic level structural information; providing links between low-resolution images of functional states of the ribosome during translocation and the near-atomic structural distortions that make up these motions; and characterizing protein-protein interfaces in assembled virus capsids from an energetic and structural standpoint, providing a basis for understanding large-scale molecular assembly. Additional research involves the ongoing development of methods for, and applications to, protein folding, loop, and homology modeling, including participation in CASP5, to perfect and Aharden@ physics-based approaches to structural genomics, and the development and testing of software to extend the range of atom-based modeling methods to larger systems.
